A comparative study of protein structure prediction tools for challenging targets: Snake venom toxins

Konstantinos Kalogeropoulos, Markus-Frederik Bohn, David E. Jenkins, Jann Ledergerber, Christoffer V. Sørensen, Nils Hofmann, Jack Wade, Thomas Fryer, Giang Thi Tuyet Nguyen, Ullrich auf dem Keller, Andreas H. Laustsen, Timothy P. Jenkins*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Protein structure determination is a critical aspect of biological research, enabling us to understand protein function and potential applications. Recent advances in deep learning and artificial intelligence have led to the development of several protein structure prediction tools, such as AlphaFold2 and ColabFold. However, their performance has primarily been evaluated on well-characterised proteins, their performance on proteins lacking experimental structures, such as many snake venom toxins, has been less scrutinised. In this study, we evaluated three modelling tools on their prediction of over 1000 snake venom toxin structures for which no experimental structures exist. Our findings show that AlphaFold2 (AF2) performed the best across all assessed parameters. We also observed that ColabFold (CF) only scored slightly worse than AF2, while being computationally less intensive. All tools struggled with regions of intrinsic disorder, such as loops and propeptide regions, and performed well in predicting the structure of functional domains. Overall, our study highlights the importance of exercising caution when working with proteins with no experimental structures available, particularly those that are large and contain flexible regions. Nonetheless, leveraging computational structure prediction tools can provide valuable insights into the modelling of protein interactions with different targets and reveal potential binding sites, active sites, and conformational changes, as well as into the design of potential molecular binders for reagent, diagnostic, or therapeutic purposes.
Original languageEnglish
Article number107559
JournalToxicon
Volume238
Number of pages25
ISSN0041-0101
DOIs
Publication statusPublished - 2024

Keywords

  • Protein structure prediction
  • Structural modelling
  • AlphaFold2
  • ColabFold
  • Modeller
  • Toxins
  • Challenging targets

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